HHsearch alignment for GI: 254780351 and conserved domain: pfam04552

>pfam04552 Sigma54_DBD Sigma-54, DNA binding domain. This DNA binding domain is based on peptide fragmentation data. This domain is proximal to DNA in the promoter/holoenzyme complex. Furthermore this region contains a putative helix-turn-helix motif. At the C-terminus, there is a highly conserved region known as the RpoN box and is the signature of the sigma-54 proteins.
Probab=90.80  E-value=0.78  Score=25.26  Aligned_cols=75  Identities=25%  Similarity=0.194  Sum_probs=42.4

Q ss_pred             CCCCHHHHHHHHCCCCCHHHHHHHHHH-H--CCCEE------EEECCCCCCEEEEEECHHHHH-HHHHHHHHHHHHHHHH
Q ss_conf             796889999985477105679999999-7--78878------863610071056445788999-9999999999999999
Q gi|254780351|r   69 LELTAGELRSRGYYLGSNVSYNLKKLI-D--LGFIK------HQRSRIDKRSIRISLTQSGKE-IAETISQLYQRHIESI  138 (171)
Q Consensus        69 ~~~t~~eLa~~l~i~~~tvs~~i~~Le-~--~G~i~------r~~~~~D~R~~~i~LT~~G~~-~~~~~~~~~~~~~~~l  138 (171)
T Consensus        48 ~PLtlk~iA~~l~lh~STVSRav~~Kyi~tp~Gi~~lk~fFs~~~~~-----------~~~~~~S~~~ik~~I~~lI~~E  116 (160)
T pfam04552        48 RPLTLREVAEALGMHESTVSRATTNKYLATPRGLFELKYFFSSAVST-----------SGGGEASATAIRALIKKLIAAE  116 (160)
T ss_pred             CCCCHHHHHHHCCCCCCHHHHHHHHHHHHCCCCEEEHHHHHHCCCCC-----------CCCCCHHHHHHHHHHHHHHHHC
T ss_conf             57619999988099810699999613976799516599985013678-----------8863022999999999999824


Q ss_pred             HHHCCCCHHHHHHHHH
Q ss_conf             8534999899999999
Q gi|254780351|r  139 DKVGGLSVDDFIAMNK  154 (171)
Q Consensus       139 ~~~~~ls~ee~~~l~~  154 (171)
T Consensus       117 d~~~PlSD~~I~~~L~  132 (160)
T pfam04552       117 DPKKPLSDDKIVELLK  132 (160)
T ss_pred             CCCCCCCHHHHHHHHH
T ss_conf             7899999999999999